No...bypass is an excellent way to do this. Note that if you can drill as shown, you do not kill the valve, you just allow partial bypass of the pump shot. The alternatives...shortening stroke to less than the Ford range or shrinking the orifice in the jet below pump both would screw up power valve function, either bringing it in too late or reducing its flow and either way leaning out the full throttle mixture.
Note how much stuff in a 97 the pump and the PV share...see the how-it-works bulletins on that!
I think there are some other factors in the problem of adapting to duals...slight leaning of jetting commonly improves things, I would guess because each carb is closer to cylinders and need less compensation for distant cylinders, though major changes from stock are I think misdirections. Duals will also of course have less airflow each and so carbs presumably run into a higher level on the idle and off-idle circuits before venturis come into play...Stromberg was thinking about that too, I believe, with the mods on the last 97's.